Once I've clicked on a joint to tell it to do something I end up unable to return it to either holding or relaxed, it instead cycling between whatever moving options it has.
Running on Windows 7 with most recent version.

Those are the new 'controls' AFAIK. Use the keyboard to make a joint hold or relax.

Yep.

Use "z" to toggle extend/contract, use "x" to toggle hold/relax and use "c" to relax- and hold all.

Meh! Is there no option to switch between controls..? I find it much more easier to use the mouse.

Nope, I don't think so. If it's a big problem, drop down a version.